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. 2021 Mar 2;11(4):jkab062. doi: 10.1093/g3journal/jkab062

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© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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RABBIT chromosome reconstructions for real-life hybrid swarm individuals. (A) Depictions of estimated haplotypes for six low-coverage F₅ Drosophila melanogaster, identified by sample number. (B) Genotype estimate concordance between our reconstruction pipeline and higher coverage genotype calls. Colors correspond to individuals 1–6 in (A). Our low-coverage genotype estimates tend to be 97–99% concordant with high-coverage calls, except in cases where RABBIT estimates are highly recombinant. A dashed line at 10 recombination events marks our threshold for excluding assumedly inaccurate hyper-recombinant reconstructions.